NAME

proteinortho6 - orthology detection tool

SYNOPSIS

proteinortho6 [OPTIONS] FASTA1 FASTA2 [FASTA...]

DESCRIPTION

Proteinortho is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. Proteinortho was applied to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. Authors succeeded identifying thirty proteins present in 99% of all bacterial proteomes.

OPTIONS

-e=

E-value for blast [default: 1e-05]

-p=

blast program {blastp+|blastn+|tblastx+|diamond|usearch|ublast|lastp|lastn|rapsearch|topaz|blatp|blatn|mmseqsp|mmseqsn} [default: diamond]

-project=

prefix for all result file names [default: myproject]

-synteny

activate PoFF extension to separate similar sequences by contextual adjacencies (requires .gff for each .fasta)

-dups=

PoFF: number of reiterations for adjacencies heuristic, to determine duplicated regions (default: 0)

-cs=

PoFF: Size of a maximum common substring (MCS) for adjacency matches (default: 3)

-alpha=

PoFF: weight of adjacencies vs. sequence similarity (default: 0.5)

-desc

write description files (for NCBI FASTA input only)

-keep

stores temporary blast results for reuse

-force

forces recalculation of blast results in any case

-cpus=

number of processors to use [default: auto]

-selfblast

apply selfblast, detects paralogs without orthologs

-singles

report singleton genes without any hit

-identity=

min. percent identity of best blast hits [default: 25]

-cov=

min. coverage of best blast alignments in % [default: 50]

-conn=

min. algebraic connectivity [default: 0.1]

-sim=

min. similarity for additional hits (0..1) [default: 0.95]

-step=

1 -> generate indices 2 -> run blast (and ff-adj, if -synteny is set) 3 -> clustering 0 -> all (default)

-binpath=

path to your local blast/diamond/... (if not installed globally)

-verbose

keeps you informed about the progress

-clean

remove all unnecessary files after processing

-debug

gives detailed information for bug tracking

More specific blast parameters can be defined by

-subparaBLAST='[parameters]' (e.g. -subparaBLAST='-seg no')

In case jobs should be distributed onto several machines, use

-jobs=M/N If you want to involve multiple machines or separate a Proteinortho run into smaller chunks, use the -jobs=M/N option. First, run 'proteinortho6.pl -steps=1 ...' to generate the indices. Then you can run 'proteinortho6.pl -steps=2 -jobs=M/N ...' to run small chunks separately. Instead of M and N numbers must be set representing the number of jobs you want to divide the run into (M) and the job division to be performed by the process.